AMBER Archive (2009)

Subject: Re: [AMBER] Coarse grained MD in AMBER ?

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Wed Jun 17 2009 - 13:57:58 CDT

AMBER is usually used for molecular dynamic simulations, with force fields
(Cornell, GAFF) implemented for atomistic simulations. For coarse-grained
simulations, depending on the timescale, other software like GROMACS,
University of Houston Brownian Dynamics, and LAMMPS are used. Your
selection of CG software depends on what coarse-grained force field you want
to use.

Since you have a protein, you may want to take a look at the MARTINI force
field, which has been successfully applied to proteins.
http://md.chem.rug.nl/~marrink/coarsegrain.html GROMACS have been used to
run these CG simulations.

2009/6/17 Siddharth Rastogi <siddharthrastogi08_at_gmail.com>

> Dear All,
>
> I want to perform a coarse grained MD of my protein of interest. I have the
> query that, whether AMBER is supported for Coarse grained MD ??
> If yes, how can I proceed for that ? Please let me know.
>
> Thanks in advance for your kind suggestions.
>
> --
> Siddharth Rastogi
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber